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Nguyen TT, Nguyen HH, Ninh HT, Le LTH, Bui HT, Orlov N, Hoang CV, Ziegler T. Zhangixalusthaoae sp. nov., a new green treefrog species from Vietnam (Anura, Rhacophoridae). Zookeys 2024; 1197:93-113. [PMID: 38628553 PMCID: PMC11019256 DOI: 10.3897/zookeys.1197.104851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 03/10/2024] [Indexed: 04/19/2024] Open
Abstract
We describe a new treefrog species from Lao Cai Province, northwestern Vietnam. The new species is assigned to the genus Zhangixalus based on a combination of the following morphological characters: (1) dorsum green, smooth; body size medium (SVL 30.1-32.2 in males); (2) fingers webbed; tips of digits expanded into large disks, bearing circum-marginal grooves; (3) absence of dermal folds along limbs; (4) absence of supracloacal fold and tarsal projection. The new species can be distinguished from its congeners by: (1) dorsal surface of the head and body green without spots; (2) axilla and groin cream with a black blotch; (3) ventral cream without spot; (4) chin creamy with grey marbling; anterior part of the thigh and ventral surface of tibia orange without spots; posterior parts of thigh orange with a large black blotch; (5) ventral side of webbing orange with some grey pattern (6) iris red-bronze, pupils black; (7) finger webbing formula I1¼-1¼II1-2III1-1IV, toe webbing formula I½-½II0-1½III¼-1¾IV1¾-½V. Phylogenetically, the new species is nested in the same subclade as Z.jodiae, Z.pinglongensis, and Z.yaoshanensis, with genetic distances ranging from 3.23% to 4.68%. The new species can be found in evergreen montane tropical forests at an elevation of about 1,883 m a.s.l. This new discovery brings the number of known genus Zhangixalus species to 42 and the number of species reported from Vietnam to 10.
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Affiliation(s)
- Tao Thien Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam Academy of Science and TechnologyHanoiVietnam
| | - Huy Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam Academy of Science and TechnologyHanoiVietnam
| | - Hoa Thi Ninh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam Academy of Science and TechnologyHanoiVietnam
| | - Linh Tu Hoang Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam Academy of Science and TechnologyHanoiVietnam
| | - Hai Tuan Bui
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam Academy of Science and TechnologyHanoiVietnam
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, 199034, St. Petersburg, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| | - Chung Van Hoang
- Forest Resources and Environment Centre, 300 Ngoc Hoi Road, Thanh Tri, Hanoi, VietnamForest Resources and Environment CentreHanoiVietnam
| | - Thomas Ziegler
- AG Zoologischer Garten Köln, Riehler Strasse 173, D-50735 Cologne, GermanyAG Zoologischer Garten KölnCologneGermany
- Institute of Zoology, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, GermanyUniversity of CologneCologneGermany
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Zhou Z, Ding L, Liu Z, Fu L, Xu L, Feng L, Yu S, Li P, Zhou Y. The complete mitochondrial genome of Goniurosaurus varius (Squamata: Eublepharidae). Mitochondrial DNA B Resour 2023; 8:1215-1219. [PMID: 38239912 PMCID: PMC10796122 DOI: 10.1080/23802359.2023.2278817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/29/2023] [Indexed: 01/22/2024] Open
Abstract
The complete mitochondrial genome sequence of Goniurosaurus varius is 17778 bp in length (GenBank accession number OQ992199), containing 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The gene order and orientation are identical to those of other Eublepharidae species in the GenBank database. Seven protein-coding genes (COX2, COX3, ND1, ND2, ND3, ND4 and CYTB) exhibit incomplete stop codon 'T.' Phylogenetic analysis revealed the monophyly of Goniurosaurus and Eublepharidae and suggested that G. varius is closely related to the lineage composed of G. luii and G. liboensis. Distinct from other published Eublepharidae species, G. varius contains an extra non-coding region between tRNA-Thr and tRNA-Pro, which may be formed by gene rearrangements. The complete mitochondrial genome will be helpful for further studies on the population genetics of this species and phylogenetic analyses of Eublepharidae.
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Affiliation(s)
- Zhengyan Zhou
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lin Ding
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Ziyi Liu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Longming Fu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lanying Xu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lin Feng
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Sufan Yu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Pipeng Li
- Institute of Herpetology, Shenyang Normal University, Shenyang, China
| | - Yu Zhou
- College of Life Science, Shenyang Normal University, Shenyang, China
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Cai LN, Zhang LH, Lin YJ, Wang JY, Storey KB, Zhang JY, Yu DN. Two-Fold ND5 Genes, Three-Fold Control Regions, lncRNA, and the "Missing" ATP8 Found in the Mitogenomes of Polypedates megacephalus (Rhacophridae: Polypedates). Animals (Basel) 2023; 13:2857. [PMID: 37760257 PMCID: PMC10525163 DOI: 10.3390/ani13182857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
In prior research on the mitochondrial genome (mitogenome) of Polypedates megacephalus, the one copy of ND5 gene was translocated to the control region (CR) and the ATP8 gene was not found. Gene loss is uncommon among vertebrates. However, in this study, we resequenced the mitogenomes of P. megacephalus from different regions using a "primer bridging" approach with Sanger sequencing technologies, which revealed the "missing" ATP8 gene in P. megacephalus as well as three other previously published Polypedates. The mitogenome of this species was found to contain two copies of the ND5 genes and three copies of the control regions. Furthermore, multiple tandem repeats were identified in the control regions. Notably, we observed that there was no correlation between genetic divergence and geographic distance. However, using the mitogenome, gene expression analysis was performed via RT-qPCR of liver samples and it was thus determined that COIII, ND2, ND4, and ND6 were reduced to 0.64 ± 0.24, 0.55 ± 0.34, 0.44 ± 0.21 and 0.65 ± 0.17, respectively, under low-temperature stress (8 °C) as compared with controls (p < 0.05). Remarkably, the transcript of long non-coding RNA (lncRNA) between positions 8029 and 8612 decreased significantly with exposure to low-temperature stress (8 °C). Antisense ND6 gene expression showed a downward trend, but this was not significant. These results reveal that modulations of protein-coding mitochondrial genes and lncRNAs of P. megacephalus play a crucial role in the molecular response to cold stress.
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Affiliation(s)
- Ling-Na Cai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou 325200, China;
| | - Yi-Jie Lin
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
| | - Jing-Yan Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Park D, Kim IH, Park IK, Grajal-Puche A, Park J. A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA. Zookeys 2022; 1129:21-35. [PMID: 36761844 PMCID: PMC9836557 DOI: 10.3897/zookeys.1129.82981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022] Open
Abstract
Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.
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Affiliation(s)
- Daesik Park
- Kangwon National University, Chuncheon, Republic of KoreaKangwon National UniversityChuncheonRepublic of Korea
| | - Il-Hun Kim
- National Marine Biodiversity Institute of Korea, Seochun, Republic of KoreaNational Marine Biodiversity Institute of KoreaSeochunRepublic of Korea
| | - Il-Kook Park
- Kangwon National University, Chuncheon, Republic of KoreaKangwon National UniversityChuncheonRepublic of Korea
| | - Alejandro Grajal-Puche
- Northern Arizona University, Flagstaff, Arizona, USANorthern Arizona UniversityFlagstaffUnited States of America
| | - Jaejin Park
- Kangwon National University, Chuncheon, Republic of KoreaKangwon National UniversityChuncheonRepublic of Korea
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Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae. Animals (Basel) 2022; 12:ani12182449. [PMID: 36139309 PMCID: PMC9494961 DOI: 10.3390/ani12182449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Duplicated control regions have been reported several times in the tree frog family Rhacophoridae, and previous studies have mostly relied on sequence analysis to reconstruct their evolution. This is the first study to employ a phylogenetic method to demonstrate the existence of concerted and parallel evolution succinctly and intuitively in the duplicated control regions of the family Rhacophoridae. Phylogenetic relationships were also used to illustrate the parallel evolution of ATP8 loss of function in the genus Polypedates. In general, this study elucidated the evolutionary patterns and pathways of mitochondrial gene rearrangement of the family Rhacophoridae from a phylogenetic perspective, which aids in understanding the evolutionary history of this fascinating tree frog taxon from a molecular evolution standpoint. Abstract New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy “LTPF” tRNA gene cluster compared to the novel “TLPF” order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.
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Xiaokaiti X, Hashiguchi Y, Ota H, Kumazawa Y. Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae. Genes (Basel) 2022; 13:genes13081470. [PMID: 36011381 PMCID: PMC9407768 DOI: 10.3390/genes13081470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.
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Affiliation(s)
- Xiakena Xiaokaiti
- Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Yasuyuki Hashiguchi
- Department of Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki 569-0801, Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, and Museum of Nature and Human Activities, Sanda 669-1546, Japan
| | - Yoshinori Kumazawa
- Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
- Correspondence: ; Tel.: +81-52-872-5844
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The mitochondrial genome and phylogenetic analysis of Rhacophorus rhodopus. Sci Rep 2022; 12:13693. [PMID: 35953583 PMCID: PMC9372073 DOI: 10.1038/s41598-022-17814-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/01/2022] [Indexed: 11/08/2022] Open
Abstract
Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.
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Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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Inagaki H, Haramoto Y, Kubota HY, Shigeri Y. Complete mitochondrial genome sequence of Japanese forest green tree frog ( Rhacophorus arboreus). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3347-3348. [PMID: 33458164 PMCID: PMC7782537 DOI: 10.1080/23802359.2020.1820396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We determined the complete mitochondrial genome sequence of the Japanese forest green tree frog (Rhacophorus arboreus). The mitochondrial genome is 22,236 bp in length, which encodes 13 protein-coding genes, 2 rRNA, and 22 tRNA genes, and two control regions (D-loops). The whole gene arrangement of R. arboreus was the same as that of Rhacophorus omeimontis and Rhacophorus schlegelii.
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Affiliation(s)
- Hidetoshi Inagaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshikazu Haramoto
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hiroshi Y Kubota
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yasushi Shigeri
- Department of Chemistry, Wakayama Medical University, Wakayama, Japan
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Bernacki LE, Kilpatrick CW. Structural Variation of the Turtle Mitochondrial Control Region. J Mol Evol 2020; 88:618-640. [PMID: 32808073 DOI: 10.1007/s00239-020-09962-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022]
Abstract
The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3' terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription.
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Affiliation(s)
- Lucas E Bernacki
- Department of Sciences, Saint Joseph's College, Mercy Hall, Rm 122, 278 Whites Bridge Road, Standish, ME, 04084, USA.
- Department of Biology, University of Vermont, Burlington, VT, USA.
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12
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Poyarkov NA, Pawangkhanant P, Gorin VA, Juthong W, Suwannapoom C. A new species of miniaturised narrow-mouth frog of the genus Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from northern Tenasserim, Thailand. J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1804005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Nikolay A. Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
- Laboratory of Tropical Ecology, Joint Russian–Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Vladislav A. Gorin
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Watinee Juthong
- Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
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13
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Nguyen TT, Ninh HT, Orlov N, Nguyen TQ, Ziegler T. A new species of the genus Zhangixalus (Amphibia: Rhacophoridae) from Vietnam. J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1754484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Tao Thien Nguyen
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hoa Thi Ninh
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Truong Quang Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thomas Ziegler
- Aquarium, AG Zoologischer Garten Köln, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
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14
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Cai YY, Shen SQ, Lu LX, Storey KB, Yu DN, Zhang JY. The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world's largest frogs. PeerJ 2019; 7:e7532. [PMID: 31497398 PMCID: PMC6709665 DOI: 10.7717/peerj.7532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/22/2019] [Indexed: 01/21/2023] Open
Abstract
The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr , tRNAPro , tRNAPhe , tRNAVal , tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).
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Affiliation(s)
- Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Shi-Qi Shen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Li-Xu Lu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
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15
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Huang A, Liu S, Li H, Luo H, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Li S, Zhang M. The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis. PeerJ 2019; 7:e7415. [PMID: 31396450 PMCID: PMC6679912 DOI: 10.7717/peerj.7415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/04/2019] [Indexed: 11/30/2022] Open
Abstract
The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.
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Affiliation(s)
- An Huang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Haijun Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongdi Luo
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Bo Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Song Li
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Mingwang Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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16
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Poyarkov NA, Gorin VA, Zaw T, Kretova VD, Gogoleva SS, Pawangkhanant P, Che J. On the road to Mandalay: contribution to the Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) fauna of Myanmar with description of two new species. Zool Res 2019; 40:244-276. [PMID: 31204803 PMCID: PMC6680123 DOI: 10.24272/j.issn.2095-8137.2019.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/07/2019] [Indexed: 11/21/2022] Open
Abstract
We present a morphological and molecular assessment of the Microhyla fauna of Myanmar based on new collections from central (Magway Division) and northern (Kachin State) parts of the country. In total, six species of Microhyla are documented, including M. berdmorei, M. heymonsi, M. butleri, M. mukhlesuri and two new species described from the semi-arid savanna-like plains of the middle part of the Irrawaddy (Ayeyarwady) River Valley. We used a 2 481 bp long 12S rRNA-16S rRNA fragment of mtDNA to hypothesize genealogical relationships within Microhyla. We applied an integrative taxonomic approach combining molecular, morphological, and acoustic lines of evidence to evaluate the taxonomic status of Myanmar Microhyla. We demonstrated that the newly discovered populations of Microhyla sp. from the Magway Division represent two yet undescribed species. These two new sympatric species are assigned to the M. achatina species group, with both adapted to the seasonally dry environments of the Irrawaddy Valley. Microhyla fodiens sp. nov. is a stout-bodied species with a remarkably enlarged shovel-like outer metatarsal tubercle used for burrowing and is highly divergent from other known congeners (P-distance≥8.8%). Microhyla irrawaddy sp. nov. is a small-bodied slender frog reconstructed as a sister species to M. kodial from southern India (P-distance=5.3%); however, it clearly differs from the latter both in external morphology and advertisement call parameters. Microhyla mukhlesuri is reported from Myanmar for the first time. We further discuss the morphological diagnostics and biogeography of Microhyla species recorded in Myanmar.
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Affiliation(s)
- Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
- Joint Russian-Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Vladislav A. Gorin
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Than Zaw
- Zoology Department, Mohnyin Degree College, Mohnyin, Kachin State 1111, Myanmar
| | - Valentina D. Kretova
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Svetlana S. Gogoleva
- Joint Russian-Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia
- Zoological Museum of the Lomonosov Moscow State University, Moscow 125009, Russia
| | | | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw 05282, Myanmar
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17
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Zhang JY, Luu BE, Yu DN, Zhang LP, Al-attar R, Storey KB. The complete mitochondrial genome of Dryophytes versicolor: Phylogenetic relationship among Hylidae and mitochondrial protein-coding gene expression in response to freezing and anoxia. Int J Biol Macromol 2019; 132:461-469. [DOI: 10.1016/j.ijbiomac.2019.03.220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 11/17/2022]
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18
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Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
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Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
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19
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Poyarkov NA, Suwannapoom C, Pawangkhanant P, Aksornneam A, Duong TV, Korost DV, Che J. A new genus and three new species of miniaturized microhylid frogs from Indochina (Amphibia: Anura: Microhylidae: Asterophryinae). Zool Res 2018; 39:130-157. [PMID: 29683109 PMCID: PMC5968859 DOI: 10.24272/j.issn.2095-8137.2018.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We report on the discovery of a new genus of microhylid subfamily Asterophryinae from northern and eastern Indochina, containing three new species. VietnamophryneGen. nov. are secretive miniaturized frogs (SVL<21 mm) with a mostly semi-fossorial lifestyle. To assess phylogenetic relationships, we studied 12S rRNA – 16S rRNA mtDNA fragments with a final alignment of 2 591 bp for 53 microhylid species. Morphological and osteological characters were analyzed using micro-CT scanning and used to describe the new genus. Results of phylogenetic analyses assigned the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Siamophryne from southern Indochina. The three specimens collected from Gia Lai Province in central Vietnam, Cao Bang Province in northern Vietnam, and Chiang Rai Province in northern Thailand proved to be separate species, different both in morphology and genetics (genetic divergence 3.1%≤P≤5.1%). Our work provides further evidence for the “out of Indo-Eurasia” scenario for Asterophryinae, indicating that the initial cladogenesis and differentiation of this group of frogs occurred in the Indochina Peninsula. To date, each of the three new species of VietnamophryneGen. nov. is known only from a single specimen; thus, their distribution, life history, and conservation status require further study.
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Affiliation(s)
- Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; E-mail:.,Joint Russian-Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Akrachai Aksornneam
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Tang Van Duong
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia.,Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dmitriy V Korost
- Petroleum Geology Department, Geological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw 05282, Myanmar
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20
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Zhang JY, Zhang LP, Yu DN, Storey KB, Zheng RQ. Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae. BMC Evol Biol 2018; 18:26. [PMID: 29486721 PMCID: PMC6389187 DOI: 10.1186/s12862-018-1140-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae. RESULTS In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis. CONCLUSIONS We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.
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Affiliation(s)
- Jia-Yong Zhang
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
| | - Dan-Na Yu
- Key lab of wildlife biotechnology, conservation and utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China.
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rong-Quan Zheng
- Xingzhi College, Zhejiang Normal University, Jinhua, Zhejiang Province, 321004, China
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21
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Suwannapoom C, Sumontha M, Tunprasert J, Ruangsuwan T, Pawangkhanant P, Korost DV, Poyarkov NA. A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand. PeerJ 2018; 6:e4422. [PMID: 29497587 PMCID: PMC5828679 DOI: 10.7717/peerj.4422] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/07/2018] [Indexed: 11/20/2022] Open
Abstract
We report on a discovery of Siamophryne troglodytesGen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA-16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytesGen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the "out of Indo-Eurasia" biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytesGen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it.
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Affiliation(s)
- Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Montri Sumontha
- Department of Fishery, Ranong Marine Fisheries Station, Ranong, Thailand
| | - Jitthep Tunprasert
- Department of Ecology, Nakhon Pathom Rajabhat University, Nakhon Pathom Mueng, Nakhon Pathom, Thailand
| | - Thiti Ruangsuwan
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Dmitriy V. Korost
- Geological Faculty, Petroleum Geology Department, Moscow State University, Moscow, Russia
| | - Nikolay A. Poyarkov
- Biological Faculty, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
- Laboratory of Tropical Ecology, Joint Russian–Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
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Jiang L, Zhao L, Cheng D, Zhu L, Zhang M, Ruan Q, Chen W. The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications. Gene 2017; 626:367-375. [PMID: 28536079 DOI: 10.1016/j.gene.2017.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/30/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
Abstract
The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.
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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China; Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Li Zhao
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Dongmei Cheng
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Lilan Zhu
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
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Chen Z, Li H, Zhu Y, Feng Q, He Y, Chen X. Molecular phylogeny of the family Dicroglossidae (Amphibia: Anura) inferred from complete mitochondrial genomes. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yuan S, Xia Y, Zheng Y, Zeng X. Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri. PeerJ 2016; 4:e2786. [PMID: 27994980 PMCID: PMC5162401 DOI: 10.7717/peerj.2786] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/11/2016] [Indexed: 01/01/2023] Open
Abstract
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.
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Affiliation(s)
- Siqi Yuan
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yun Xia
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
| | - Yuchi Zheng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
| | - Xiaomao Zeng
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China
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Wei M, Liu Y, Guo H, Zhao F, Chen S. Characterization of the complete mitochondrial genome of Cynoglossus gracilis and a comparative analysis with other Cynoglossinae fishes. Gene 2016; 591:369-75. [PMID: 27312953 DOI: 10.1016/j.gene.2016.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 11/29/2022]
Abstract
Mitochondrial genomes can provide basic information for phylogenetic analysis and evolutionary studies. We present here the mitochondrial genome of Cynoglossus gracilis, which is 16,565bp in length. Numerous distinct regions were identified, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, a light-strand replication origin, and a control region. Interestingly, we detected rearrangement of genes in C. gracilis, including a control region translocation, tRNA(Gln) gene inversion, and tRNA(Ile) gene shuffling. Additionally, a phylogenetic analysis based on the nucleotide sequences of the 13 PCGs using maximum likelihood and Bayesian inference methods reveals that C. gracilis is closely related to Cynoglossus semilaevis. This study provides important mitogenomic data for analyzing phylogenetic relationships in the Cynoglossinae.
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Affiliation(s)
- Min Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Yang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Hua Guo
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Fazhen Zhao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Songlin Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
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Gomes C, Rodrigues-Filho LF, Sodré D, Neckel-Oliveira S, Gordo M, Gallati U, Sequeira F, Vallinoto M. Concerted evolution in the mitochondrial control region of the Amazon small-bodied frog Pseudopaludicola canga (Anura, Leiuperidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4270-4273. [PMID: 27206788 DOI: 10.3109/19401736.2015.1060477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study presents evidence of concerted evolution in the mitochondrial control region of the frog Pseudopaludicola canga. Four repeat units of 88 bp (as well as a fifth, incomplete unit) were observed in the 5' domain, with the duplicated segments of the same specimen being more related to one another than to the equivalent regions in other specimens, as a result of concerted evolution. We highlight that drawing conclusions from phylogeographical analysis using the control region containing VNTRs must be interpreted with caution, because it violated a basic assumption of phylogeny, since the regions cannot be treated as independent characters.
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Affiliation(s)
- Camila Gomes
- a Laboratório de Evolução , Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará , Bragança Campus, Bragança-PA , Brazil
| | - Luis Fernando Rodrigues-Filho
- a Laboratório de Evolução , Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará , Bragança Campus, Bragança-PA , Brazil
| | - Davidson Sodré
- a Laboratório de Evolução , Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará , Bragança Campus, Bragança-PA , Brazil
| | - Selvino Neckel-Oliveira
- b Departamento de Ecologia e Zoologia , Centro de Ciências Biológicas, Universidade Federal de Santa Catarina , Florianópolis, SC , Brazil
| | - Marcelo Gordo
- c Departamento de Biologia , Instituto de Ciências Biológicas, Universidade Federal do Amazonas , Manaus , AM , Brazil
| | - Ulisses Gallati
- d Coordenação de Zoologia, Museu Paraense Emilio Goeldi , Belém, PA , Brazil , and
| | - Fernando Sequeira
- e CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão , Universidade do Porto, Vairão , Portugal
| | - Marcelo Vallinoto
- a Laboratório de Evolução , Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará , Bragança Campus, Bragança-PA , Brazil.,e CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão , Universidade do Porto, Vairão , Portugal
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Huang M, Lv T, Duan R, Zhang S, Li H. The complete mitochondrial genome of Rhacophorus dennysi (Anura: Rhacophoridae) and phylogenetic analysis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3719-20. [PMID: 26329505 DOI: 10.3109/19401736.2015.1079873] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Rhacophorus dennysi is one species of the family Rhacophoridae. In this study, we sequenced the complete mitochondrial genome of R. dennysi. The complete mitochondrial genome of R. dennysi was 17 572 bp in length (GenBank accession number KT191129). Similar to the typical mtDNA of amphibians, the complete mtDNA sequence of R. dennysi contained two rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and one D-loop region. The complete mitogenome sequence data in R. dennysi would provide a basis and important molecular data for studying the phylogenetic relationship, molecular identification and evolutionary analysis in anura species. The results will be useful for the detailed study of mitogenome evolution and the phylogenetic relationships among the orders in the class Rhacophoridae.
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Affiliation(s)
- Minyi Huang
- a College of Life Science, Anqing Normal University , Anqing , China and
| | - Tong Lv
- b School of Life Science and Technology, Tongji Universtity , Shanghai , China
| | - Renyan Duan
- a College of Life Science, Anqing Normal University , Anqing , China and
| | - Siyu Zhang
- a College of Life Science, Anqing Normal University , Anqing , China and
| | - Hairong Li
- a College of Life Science, Anqing Normal University , Anqing , China and
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Stokkan M, Jurado-Rivera JA, Juan C, Jaume D, Pons J. Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome gene orders in the genus Pseudoniphargus (Crustacea: Amphipoda). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3579-89. [PMID: 26329687 DOI: 10.3109/19401736.2015.1079821] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A comparison of mitochondrial genomes of three species of the amphipod Pseudoniphargus revealed the occurrence of a surprisingly high level of gene rearrangement involving protein-coding genes that is a rare phenomenon at low taxonomic levels. The three Pseudoniphargus mitogenomes also display a unique gene arrangement with respect to either the presumed Pancrustacean order or those known for other amphipods. Relative long non-coding sequences appear adjacent to the putative breakage points involved in gene rearrangements of protein coding genes. Other details of the newly obtained mitochondrial genomes - e.g., gene content, nucleotide composition and codon usage - are similar to those found in the mitogenomes of other amphipod species studied. They all contain the typical mitochondrial genome set consisting of 13 protein-coding genes, 22 tRNAs, and two rRNAS, as well as a large control region. The secondary structures and characteristics of tRNA and ribosomal mitochondrial genes of these three species are also discussed.
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Affiliation(s)
- Morten Stokkan
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and
| | - Jose A Jurado-Rivera
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and.,b Departament de Biologia , Universitat de les Illes Balears , Palma , Spain
| | - Carlos Juan
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and.,b Departament de Biologia , Universitat de les Illes Balears , Palma , Spain
| | - Damià Jaume
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and
| | - Joan Pons
- a Department of Biodiversity and Conservation , Instituto Mediterraneo de Estudios Avanzados (IMEDEA, CSIC-UIB) , Esporles , Spain and
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29
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Shi W, Gong L, Wang SY, Miao XG, Kong XY. Tandem Duplication and Random Loss for mitogenome rearrangement in Symphurus (Teleost: Pleuronectiformes). BMC Genomics 2015; 16:355. [PMID: 25943439 PMCID: PMC4430869 DOI: 10.1186/s12864-015-1581-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial genomes (mitogenomes) of flatfishes (Pleuronectiformes) exhibit highly diversified types of large-scale gene rearrangements. We have reported that the mitogenomes of Crossorhombus azureus (Bothidae), Samariscus latus (Samaridae) and Cynoglossus fishes (Cynoglossidae) show different types of gene rearrangements. Results In the present study, the complete mitogenomes of two Symphurus species (Cynoglossidae), Symphurus plagiusa and Symphurus orientalis, were determined. The gene order in the S. plagiusa mitogenome is the same as that of a typical vertebrate (without any gene rearrangements). Surprisingly, large-scale gene rearrangements have occurred in S. orientalis. In the rearranged fragment from the control region (CR) to the WANCY tRNA cluster (tRNA cluster of tRNA-W, tRNA-A, tRNA-N, tRNA-C and tRNA-Y) in the S. orientalis mitogenome, tRNA-V and tRNA-M have been translocated to the 3’ end of the 16S rRNA gene, with six large intergenic spacers over 20 bp in length. In addition, an origin for light-strand replication (OL) structure that is typically located in the WANCY region was absent in both the S. plagiusa and S. orientalis mitogenomes. It is generally recognized that a sequence in the WANCY region that encodes tRNAs forms a hairpin structure (OL-like structure) and can act as the OL when the typical locus is lost. Moreover, an additional OL-like structure was identified near the control region in the S. plagiusa mitogenome. Conclusions The positions of the intergenic spacers and the rearranged genes of the S. orientalis mitogenome strongly indicate that the mechanism underlying the rearrangement of this mitogenome was Tandem Duplication and Random Loss. Additionally, two OL-like regions substituting for the typical locus were found in the S. plagiusa mitogenome. We speculate that the ancestral mitogenomes of S. plagiusa and S. orientalis also had this characteristic, such that if both OL-like structures functioned during mitochondrial replication, they could initiate duplicate replications of the light strand (L-strand), leading to duplication of the region between the two structures. We consider that this mechanism may account for the gene duplication that occurred during the gene rearrangement process in the evolution of the ancestral mitogenome to the S. orientalis mitogenome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1581-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Li Gong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Shu-Ying Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Xian-Guang Miao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Xiao-Yu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
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Ding L, Chen C, Wang H, Zhang B. Complete mitochondrial DNA sequence of Lepus tolai (Leporidae: Lepus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2085-6. [PMID: 25391036 DOI: 10.3109/19401736.2014.982568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of tolai hare, Lepus tolai (Leporidae: Lepus) by using polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 17,472 bp long and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA gens and one long non-coding region known as the control region.
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Affiliation(s)
- Ling Ding
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
| | - Changmao Chen
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
| | - Hui Wang
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
| | - Baowei Zhang
- a School of Life Sciences, Anhui University , Hefei , Anhui , China
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31
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Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of Occidozyga martensii. J Genet 2014; 93:631-41. [DOI: 10.1007/s12041-014-0418-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Xia Y, Zheng Y, Miura I, Wong PBY, Murphy RW, Zeng X. The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization. BMC Genomics 2014; 15:691. [PMID: 25138662 PMCID: PMC4153901 DOI: 10.1186/1471-2164-15-691] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 08/12/2014] [Indexed: 11/25/2022] Open
Abstract
Background Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage. Results Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and dN/dS ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated. Conclusions No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-691) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 2014; 15:573. [PMID: 25001581 PMCID: PMC4111848 DOI: 10.1186/1471-2164-15-573] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
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Affiliation(s)
- Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
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Shi W, Miao XG, Kong XY. A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes). BMC Genomics 2014; 15:352. [PMID: 24885702 PMCID: PMC4035078 DOI: 10.1186/1471-2164-15-352] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 04/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements. RESULTS In the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained. CONCLUSIONS We propose a "Double Replications and Random Loss" model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.
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Affiliation(s)
| | | | - Xiao-Yu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China.
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Kakehashi R, Kurabayashi A, Oumi S, Katsuren S, Hoso M, Sumida M. Mitochondrial genomes of Japanese Babina frogs (Ranidae, Anura): unique gene arrangements and the phylogenetic position of genus Babina. Genes Genet Syst 2014; 88:59-67. [PMID: 23676710 DOI: 10.1266/ggs.88.59] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genus Babina is a member of Ranidae, a large family of frogs, currently comprising 10 species. Three of them are listed as endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered species, we determined the complete nucleotide sequences of the mt genomes of 3 endangered Japanese Babina frogs, B. holsti, B. okinavana, and B. subaspera and 1 ranid frog Lithobates catesbeianus. The genes of NADH dehydrogenase subunit 5 (nad5) and the control region (CR) were found to have high sequence divergences and to be usable for population genetics studies. At present, no consensus on the phylogenetic position of genus Babina has been reached. To resolve this problem, we performed molecular phylogenetic analyses with the largest dataset used to date (11,345 bp from 2 ribosomal RNA- and 13 protein-encoding genes) in studies dealing with Babina phylogeny. These analyses revealed monophyly of Babina and Odorrana. It is well known that mt gene rearrangements of animals can provide usable phylogenetic information. Thus, we also compared the mt gene arrangements among Babina species and other related genera. Of the surveyed species, only L. catesbeianus manifested typical neobatrachian-type mt gene organization. In the B. okinavana, an additional pseudogene of tRNA-His (trnH) was observed in the CR downstream region. Furthermore, in the B. holsti and B. subaspera, the trnH/nad5 block was translocated from its typical position to the CR downstream region, and the translocated trnH became a pseudogene. The position of the trnH pseudogene is consistent with the translocated trnH position reported in Odorrana. Consequently, the trnH rearrangement seems to be a common ancestry characteristic (synapomorphy) of Babina and Odorrana. Based on the "duplication and deletion" gene rearrangement model, a single genomic duplication event can explain the order of derived mt genes found in Babina and Odorrana.
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Affiliation(s)
- Ryosuke Kakehashi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan
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Li J, Yin W, Xia R, Lei G, Fu C. Complete mitochondrial genome of a brown frog, Rana kunyuensis (Anura: Ranidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:34-5. [PMID: 24438268 DOI: 10.3109/19401736.2013.869681] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The first complete mitochondrial genome (mitogenome) of Rana sensu stricto (sensu Frost, 2013) was determined using Rana kunyuensis as a representative species. The mitogenome was 22,255 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and duplicated control regions. The mitogenome of R. kunyuensis showed novel gene order arrangement with a translocation of tRNA(Leu)((CUN)) and ND5 in comparison with published anuran mitogenomes to date. This mitogenome should contribute to understand the evolution of anuran mitochondrial gene order arrangements.
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Affiliation(s)
- Jiao Li
- a School of Nature Conservation, Beijing Forestry University , Beijing 100083 , China and
| | - Wei Yin
- b Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering , and Institute of Biodiversity Science, Fudan University , Shanghai , China
| | - Rong Xia
- b Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering , and Institute of Biodiversity Science, Fudan University , Shanghai , China
| | - Guangchun Lei
- a School of Nature Conservation, Beijing Forestry University , Beijing 100083 , China and
| | - Cuizhang Fu
- b Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering , and Institute of Biodiversity Science, Fudan University , Shanghai , China
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Irisarri I, San Mauro D, Abascal F, Ohler A, Vences M, Zardoya R. The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates. BMC Genomics 2012; 13:626. [PMID: 23153022 PMCID: PMC3551647 DOI: 10.1186/1471-2164-13-626] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/04/2012] [Indexed: 01/20/2023] Open
Abstract
Background Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians. Results We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia. Conclusions Through the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.
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Affiliation(s)
- Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
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Cooke GM, King AG, Johnson RN, Boles WE, Major RE. Rapid characterization of mitochondrial genome rearrangements in Australian songbirds using next-generation sequencing technology. J Hered 2012; 103:882-6. [PMID: 23125406 DOI: 10.1093/jhered/ess091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using next-generation sequencing technology, we describe the complete mitochondrial genomes for 5 Australian passerine birds (Epthianura albifrons, Petroica phoenicea, Petroica goodenovii, Petroica boodang, and Eopsaltria australis). We successfully assemble each mitogenome de novo using just 1/8th of a Roche GL FSX 454 pyrosequencing plate. From the assembled mitogenomes, we identify 2 different mitochondrial gene arrangements in the region spanning 5'-3' from Cytochrome B to 12s RNA. These gene arrangements represent 2 of the 4 known avian mitochondrial gene arrangements. Our results, together with other previously described avian mitogenomes, highlight that certain mitochondrial rearrangements appear to have arisen multiple times.
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Affiliation(s)
- Georgina M Cooke
- Australian Museum, 6 College Street, Sydney, NSW 2010, Australia
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Matsui M, Hamidy A, Belabut DM, Ahmad N, Panha S, Sudin A, Khonsue W, Oh HS, Yong HS, Jiang JP, Nishikawa K. Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy. Mol Phylogenet Evol 2011; 61:167-76. [DOI: 10.1016/j.ympev.2011.05.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/24/2011] [Accepted: 05/25/2011] [Indexed: 11/28/2022]
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Nishizawa T, Kurabayashi A, Kunihara T, Sano N, Fujii T, Sumida M. Mitochondrial DNA diversification, molecular phylogeny, and biogeography of the primitive rhacophorid genus Buergeria in East Asia. Mol Phylogenet Evol 2011; 59:139-47. [DOI: 10.1016/j.ympev.2011.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 10/27/2010] [Accepted: 01/27/2011] [Indexed: 10/18/2022]
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41
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Irisarri I, San Mauro D, Green DM, Zardoya R. The complete mitochondrial genome of the relict frog Leiopelma archeyi: insights into the root of the frog Tree of Life. ACTA ACUST UNITED AC 2011; 21:173-82. [PMID: 20958226 DOI: 10.3109/19401736.2010.513973] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Determining the root of the anuran Tree of Life is still a contentious and open question in frog systematics. Two genera with disjunct distributions have been traditionally considered the most basal among extant frogs: Leiopelma, which is endemic to New Zealand, and Ascaphus, which lives in North America. However, their specific phylogenetic position is rather elusive because each genus shows many autapomorphies, and together they retain many symplesiomorphic characters. Therefore, several alternative hypotheses have been proposed regarding the relative phylogenetic position of both Leiopelma and Ascaphus. In order to distinguish among these competing phylogenetic hypotheses, we sequenced the complete mitochondrial (mt) genome of Leiopelma archeyi and used it along with previously reported frog mt genomes (including that of Ascaphus truei) to infer a robust phylogeny of major anuran lineages. The reconstructed maximum likelihood and Bayesian inference phylogenies recovered identical topology, which supports the sister group relationship of Ascaphus and Leiopelma, and the placement of this clade at the base of the anuran tree. Interestingly, the mt genome of L. archeyi displays a novel gene arrangement in frog mt genomes affecting the relative position of cytochrome b, trnT, NADH dehydrogenase subunit 6, trnE, and trnP genes. The tandem duplication-random loss model of gene order change explains the origin of this novel frog mt genome arrangement, which is convergent with others reported in some fishes and salamanders. These results, together with comparative data for other available vertebrate mt genomes, provide evidence that the 5' end of the control region is a hot spot for gene order rearrangement.
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Affiliation(s)
- Iker Irisarri
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain.
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Alam MS, Kurabayashi A, Hayashi Y, Sano N, Khan MR, Fujii T, Sumida M. Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh. Genes Genet Syst 2011; 85:219-32. [PMID: 21041980 DOI: 10.1266/ggs.85.219] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We determined the complete nucleotide sequences of mitochondrial (mt) genomes from two dicroglossid frogs, Hoplobatrachus tigerinus (Indian Bullfrog) and Euphlyctis hexadactylus (Indian Green frog). The genome sizes are 20462 bp in H. tigerinus and 20280 bp in E. hexadactylus. Although both genomes encode the typical 37 mt genes, the following unique features are observed: 1) the ND5 genes are duplicated in H. tigerinus that have completely identical sequences, whereas duplicated ND5 genes in E. hexadactylus possessed dissimilar substitutions; 2) duplicated control region (CR) in H. tigerinus has almost identical sequences whereas single control region (CR) was found in E. hexadactylus; 3) the tRNA-Leu (CUN) gene is translocated from the LTPF tRNA cluster to downstream of ND5-1 in H. tigerinus, and the tRNA-Pro gene is translocated from the LTPF tRNA cluster to downstream of CR in E. hexadactylus; 4) pseudo tRNA-Leu (CUN) and tRNA-Pro genes are observed in E. hexadactylus; and 5) two tRNA-Met genes are encoded in both species, as observed in the previously reported dicroglossid mt genomes. Almost all observed gene rearrangements in H. tigerinus and E. hexadactylus can be explained by the tandem duplication and random loss model, except translocation of tRNA-Pro in E. hexadactylus. The novel mt genomic features found in this study may be useful for future phylogenetic studies in the dicroglossid taxa. However, the mt genome with interesting features found in the present study reveal a high level of variation of gene order and gene content, inspiring more research to understand the mechanisms behind gene and genome evolution in the dicroglossid and as well as in the amphibian taxa in future studies.
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Affiliation(s)
- Mohammad Shafiqul Alam
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Japan
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43
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Eda M, Kuro-o M, Higuchi H, Hasegawa H, Koike H. Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses). Genes Genet Syst 2010; 85:129-39. [PMID: 20558899 DOI: 10.1266/ggs.85.129] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.
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Affiliation(s)
- Masaki Eda
- Graduate School of Social and Cultural Studies, Kyusyu University.
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44
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Kurabayashi A, Yoshikawa N, Sato N, Hayashi Y, Oumi S, Fujii T, Sumida M. Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids. Mol Phylogenet Evol 2010; 56:543-53. [DOI: 10.1016/j.ympev.2010.01.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 12/21/2009] [Accepted: 01/20/2010] [Indexed: 11/29/2022]
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Nilsson MA. The structure of the Australian and South American marsupial mitochondrial control region. ACTA ACUST UNITED AC 2010; 20:126-38. [PMID: 19900062 DOI: 10.3109/19401730903180112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND AIMS The mitochondrial control region (CR) was studied across five marsupialian orders, in order to give a detailed overview of its features. RESULTS The CR is organised into three domains similar to the CR of placental mammals. However, the conservation of different features among the marsupial orders is in general more strict. In the first domain, two conserved blocks extended termination-associated sequences (ETAS 1 and ETAS 2) are present in all marsupial orders. In the third domain, the three conserved sequence blocks (CSB 1, CSB 2 and CSB 3) are present and complete, with CSB 1 being duplicated in four of five marsupial orders. CONCLUSIONS The nucleotide frequency and secondary structures of the repeats were typical for marsupial species. The repeats are generally AT-rich except in Dasyuridae and Paucituberculata, which show a significant increase in GC content.
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Affiliation(s)
- Maria A Nilsson
- Institute for Experimental Pathology/ZMBE, University of Münster, Münster, Germany.
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46
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Cho HJ, Eda M, Nishida S, Yasukochi Y, Chong JR, Koike H. Tandem duplication of mitochondrial DNA in the black-faced spoonbill, Platalea minor. Genes Genet Syst 2010; 84:297-305. [PMID: 20057167 DOI: 10.1266/ggs.84.297] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial (mt) heteroplasmy in the control region (CR) of the black-faced spoonbill was investigated using LA-PCR. To avoid amplification of transpositioned nuclear genome fragment from mtDNA (numt), PCR product of the almost-complete mitochondrial genome was amplified using primers designed to anneal on the COIII gene. Then nested LA-PCR product was amplified between the cyt b and 12S rRNA genes using the almost-complete mitochondrial genome PCR product as a template. Nucleotide sequencing revealed tandem duplication composed of two units. The first contains cyt b-1, tRNA(Thr)-1, tRNA(Pro)-1, ND6-1, tRNA(Glu)-1 and CR1, and the second consists of cyt b-2, tRNA(Thr)-2, tRNA(Pro)-2, ND6-2, tRNA(Glu)-2 and CR2, followed by tRNA(Phe) and 12S rRNA. The duplicated cyt b-2 sequence coincided with 499 bp at the 3' end of cyt b-1. With the exception of the CR, the other genes in the duplicated sequence were identical to the original corresponding gene. Even though both CR1 and CR2 contain functional blocks, such as a poly-C site, a goose hairpin and a TAS structure in Domain I, the 3' end of CR1 was followed by a 112 bp sequence (non-coding region) that was not found in CR2 or in sequence homology analysis of similar genes. Meanwhile, CR2 ended in a complicated repeat sequence. The 5' franking region in the Domain I (Region A) and the 3' franking region in the Domain I (Region B) of the two CRs evolve in quite different manners: Region A was highly variable between CR1 and CR2 in the same individuals, while Region B was almost identical between them, which indicates concerted evolution.
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Affiliation(s)
- Hyong-Ju Cho
- Laboratory of Biodiversity, Department Environmental Changes, SCS, Kyushu University, Fukuoka City 819-0395, Japan
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47
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Unexpectedly high genetic diversity of mtDNA control region through severe bottleneck in vulnerable albatross Phoebastria albatrus. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0011-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae). Gene 2009; 447:86-96. [PMID: 19631263 DOI: 10.1016/j.gene.2009.07.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 03/28/2009] [Accepted: 07/14/2009] [Indexed: 11/22/2022]
Abstract
The mt genome of Paa spinosa (Anura: Ranoidae) is a circular molecule of 18,012 bp in length, containing 38 genes (including an extra copy of tRNA-Met gene). This mt genome is characterized by three distinctive features: a cluster of rearranged tRNA genes (LTPF tRNA gene cluster), a tandem duplication of tRNA-Met gene (Met1 and Met2), and distinct repeat regions at both 5' and 3'-sides in the control region. Comparing the locations and the sequences of all tRNA-Met genes among Ranoidae, and constructing NJ tree of the nucleotide of those tRNA-Met genes, we suggested a tandem duplication of tRNA-Met gene can be regarded as a synapomorphy of Dicroglossinae. To further investigate the phylogenetic relationships of anurans, phylogenetic analyses (BI, ML and MP) based on the nucleotide dataset and the corresponding amino acid dataset of 11 protein-coding genes (except ND5 and ATP8) arrived at the similar topology.
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Ren Z, Zhu B, Ma E, Wen J, Tu T, Cao Y, Hasegawa M, Zhong Y. Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications. Gene 2009; 441:148-55. [DOI: 10.1016/j.gene.2008.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2008] [Revised: 09/08/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
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50
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